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1

How to deal with large models?

Hlavacek, William S

Journal:

Molecular Systems Biology

Year:

2009

Language:

english

File:

PDF, 86 KB

english, 2009

2

[Methods in Molecular Biology] Modeling Biomolecular Site Dynamics Volume 1945 (Methods and Protocols) ||

Hlavacek, William S.

Year:

2019

Language:

english

File:

PDF, 17.54 MB

english, 2019

3

[Methods in Molecular Biology] Modeling Biomolecular Site Dynamics Volume 1945 (Methods and Protocols) || VeriFuzz: Program Aware Fuzzing

Hlavacek, William S.

Year:

2019

Language:

english

File:

PDF, 440 KB

english, 2019

4

Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks

Lin, Yen Ting, Hlavacek, William S.

Journal:

The Journal of Chemical Physics

Year:

2019

Language:

english

File:

PDF, 3.27 MB

english, 2019

5

The complexity of complexes in signal transduction

William S. Hlavacek, James R. Faeder, Michael L. Blinov, Alan S. Perelson, Byron Goldstein

Journal:

Biotechnology and Bioengineering

Year:

2003

Language:

english

File:

PDF, 339 KB

english, 2003

6

Rule-based modeling of biochemical networks

James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek

Journal:

Year:

2005

Language:

english

File:

PDF, 242 KB

english, 2005

7

Kinetic Proofreading in Receptor-Mediated Transduction of Cellular Signals: Receptor Aggregation, Partially Activated Receptors, and Cytosolic Messengers

William S. Hlavacek, Antonio Redondo, Carla Wofsy, Byron Goldstein

Journal:

Bulletin of Mathematical Biology

Year:

2002

Language:

english

File:

PDF, 291 KB

english, 2002

8

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek

Journal:

Year:

2006

Language:

english

File:

PDF, 593 KB

english, 2006

9

Hierarchical graphs for rule-based modeling of biochemical systems

Nathan W Lemons, Bin Hu, William S Hlavacek

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 429 KB

english, 2011

10

Stochastic effects and bistability in T cell receptor signaling

Tomasz Lipniacki, Beata Hat, James R. Faeder, William S. Hlavacek

Journal:

Journal of Theoretical Biology

Year:

2008

Language:

english

File:

PDF, 2.05 MB

english, 2008

11

Depicting signaling cascades

Blinov, Michael L., Yang, Jin, Faeder, James R., Hlavacek, William S.

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 103 KB

english, 2006

12

'On-the-fly' or 'generate-first' modeling?

Blinov, Michael L., Faeder, James R., Yang, Jin, Goldstein, Byron, Hlavacek, William S.

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 97 KB

english, 2005

13

Design of gene circuits: lessons from bacteria

Wall, Michael E., Hlavacek, William S., Savageau, Michael A.

Journal:

Nature Reviews Genetics

Year:

2004

Language:

english

File:

PDF, 185 KB

english, 2004

14

Mathematical and computational models of immune-receptor signalling

Goldstein, Byron, Faeder, James R., Hlavacek, William S.

Journal:

Nature Reviews Immunology

Year:

2004

Language:

english

File:

PDF, 307 KB

english, 2004

15

Reconstruction of Metabolic Networks from High-Throughput Metabolite Profiling Data : In Silico Analysis of Red Blood Cell Metabolism

ILYA NEMENMAN, G. SEAN ESCOLA, WILLIAM S. HLAVACEK, PAT J. UNKEFER, CLIFFORD J. UNKEFER, MICHAEL E. WALL

Journal:

Annals of the New York Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 493 KB

english, 2007

16

Rule-based modeling of signal transduction

James Faeder, Michael Monine, Ambarish Nag, Byron Goldstein, William Hlavacek

Journal:

Journal of Critical Care

Year:

2007

Language:

english

File:

PDF, 86 KB

english, 2007

17

RuleMonkey: software for stochastic simulation of rule-based models

Joshua Colvin, Michael I Monine, Ryan N Gutenkunst, William S Hlavacek, Daniel D Von Hoff, Richard G Posner

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 552 KB

english, 2010

18

Subunit Structure of Regulator Proteins Influences the Design of Gene Circuitry: Analysis of Perfectly Coupled and Completely Uncoupled Circuits

William S. Hlavacek, Michael A. Savageau

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 520 KB

english, 1995

19

Rules for Coupled Expression of Regulator and Effector Genes in Inducible Circuits

William S. Hlavacek, Michael A. Savageau

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 737 KB

english, 1996

20

Completely uncoupled and perfectly coupled gene expression in repressible systems

William S. Hlavacek, Michael A. Savageau

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 576 KB

english, 1997

21

The Brucella TIR-like protein TcpB interacts with the death domain of MyD88

Anu Chaudhary, Kumkum Ganguly, Stéphanie Cabantous, Geoffrey S. Waldo, Sofiya N. Micheva-Viteva, Kamalika Nag, William S. Hlavacek, Chang-Shung Tung

Journal:

Biochemical and Biophysical Research Communications

Year:

2012

Language:

english

File:

PDF, 782 KB

english, 2012

22

Multiple Functions of a Feed-Forward-Loop Gene Circuit

Michael E. Wall, Mary J. Dunlop, William S. Hlavacek

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 516 KB

english, 2005

23

Scaffold-mediated nucleation of protein signaling complexes: Elementary principles

Jin Yang, William S. Hlavacek

Journal:

Mathematical Biosciences

Year:

2011

Language:

english

File:

PDF, 512 KB

english, 2011

24

Design Principles for Regulator Gene Expression in a Repressible Gene Circuit

Michael E. Wall, William S. Hlavacek, Michael A. Savageau

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 482 KB

english, 2003

25

Retention of antigen on follicular dendritic cells and B lymphocytes through complement-mediated multivalent ligand–receptor interactions: theory and application to HIV treatment

William S. Hlavacek, Jerome K. Percus, Ora E. Percus, Alan S. Perelson, Carla Wofsy

Journal:

Mathematical Biosciences

Year:

2002

Language:

english

File:

PDF, 177 KB

english, 2002

26

A quantitative approach for studying IgE–FcεRI aggregation

Richard G Posner, Paul B Savage, Adam S Peters, Angelica Macias, Jamael DelGado, Gordon Zwartz, Larry A Sklar, William S Hlavacek

Journal:

Molecular Immunology

Year:

2002

Language:

english

File:

PDF, 141 KB

english, 2002

27

Modeling the early signaling events mediated by FcεRI

Byron Goldstein, James R. Faeder, William S. Hlavacek, Michael L. Blinov, Antonio Redondo, Carla Wofsy

Journal:

Molecular Immunology

Year:

2002

Language:

english

File:

PDF, 239 KB

english, 2002

28

Computational model for autophagic vesicle dynamics in single cells

Martin, Katie R., Barua, Dipak, Kauffman, Audra L., Westrate, Laura M., Posner, Richard G., Hlavacek, William S., MacKeigan, Jeffrey P.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.49 MB

english, 2013

29

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

Monine, Michael I., Posner, Richard G., Savage, Paul B., Faeder, James R., Hlavacek, William S.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 451 KB

english, 2010

30

Quantifying Aggregation of IgE-FcϵRI by Multivalent Antigen

Hlavacek, William S., Perelson, Alan S., Sulzer, Bernhard, Bold, Jennifer, Paar, Jodi, Gorman, Wendy, Posner, Richard G.

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 150 KB

english, 1999

31

Steric Effects on Multivalent Ligand-Receptor Binding: Exclusion of Ligand Sites by Bound Cell Surface Receptors

Hlavacek, William S., Posner, Richard G., Perelson, Alan S.

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 233 KB

english, 1999

32

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

Matthew S Creamer, Edward C Stites, Meraj Aziz, James A Cahill, Chin Wee Tan, Michael E Berens, Haiyong Han, Kimberley J Bussey, Daniel D Von Hoff, William S Hlavacek, Richard G Posner

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 644 KB

english, 2012

33

On Imposing Detailed Balance in Complex Reaction Mechanisms

Yang, Jin, Bruno, William J., Hlavacek, William S., Pearson, John E.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 103 KB

english, 2006

34

Exploring higher-order EGFR oligomerisation and phosphorylation—a combined experimental and theoretical approach

Kozer, Noga, Barua, Dipak, Orchard, Suzanne, Nice, Eduoard C., Burgess, Antony W., Hlavacek, William S., Clayton, Andrew H. A.

Journal:

Molecular BioSystems

Year:

2013

Language:

english

File:

PDF, 2.35 MB

english, 2013

35

Large Scale, High Resolution Models of Receptor Tyrosine Kinase Signaling Networks

Stites, Edward C., Creamer, Matthew S., Aziz, Meraj, Hlavacek, William S., Posner, Richard G.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 48 KB

english, 2012

36

Perspective on the q-bio Summer School and Conference: 2007–2014 and beyond

Resnekov, Orna, Munsky, Brian, Hlavacek, William S.

Journal:

Quantitative Biology

Year:

2014

Language:

english

File:

PDF, 210 KB

english, 2014

37

Interaction of a Monoclonal IgE-Specific Antibody with Cell-Surface IgE−FcεRI: Characterization of Equilibrium Binding and Secretory Response †

Posner, Richard G., Paar, Jodi M., Licht, Arieh, Pecht, Israel, Conrad, Daniel H., Hlavacek, William S.

Journal:

Year:

2004

Language:

english

File:

PDF, 104 KB

english, 2004

38

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

Chylek, Lily A., Harris, Leonard A., Tung, Chang-Shung, Faeder, James R., Lopez, Carlos F., Hlavacek, William S.

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2014

Language:

english

File:

PDF, 1.21 MB

english, 2014

39

Optimal Aggregation of FcεRI with a Structurally Defined Trivalent Ligand Overrides Negative Regulation Driven by Phosphatases

Mahajan, Avanika, Barua, Dipak, Cutler, Patrick, Lidke, Diane S., Espinoza, Flor A., Pehlke, Carolyn, Grattan, Rachel, Kawakami, Yuko, Tung, Chang-Shung, Bradbury, Andrew R. M., Hlavacek, William S.,

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 8.66 MB

english, 2014

40

Recruitment of the Adaptor Protein Grb2 to EGFR Tetramers

Kozer, Noga, Barua, Dipak, Henderson, Christine, Nice, Edouard C., Burgess, Antony W., Hlavacek, William S., Clayton, Andrew H. A.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.09 MB

english, 2014

41

Kinetic Monte Carlo method for rule-based modeling of biochemical networks

Yang, Jin, Monine, Michael I., Faeder, James R., Hlavacek, William S.

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 195 KB

english, 2008

42

The Seventh q-bio Conference: meeting report and preface

Nemenman, Ilya, Faeder, James R, Gnanakaran, S, Hlavacek, William S, Munsky, Brian, Wall, Michael E, Jiang, Yi

Journal:

Physical Biology

Year:

2014

Language:

english

File:

PDF, 921 KB

english, 2014

43

What is aortic overriding?

Anderson, Robert H., Spicer, Diane E., Henry, G. William, Rigsby, Cynthia, Hlavacek, Anthony M., Mohun, Timothy J.

Journal:

Cardiology in the Young

Year:

2015

Language:

english

File:

PDF, 2.77 MB

english, 2015

44

The significance of aortic overriding and pulmonary stenosis in tetralogy of Fallot

Anderson, Robert H., Spicer, Diane E., Henry, G. William, Rigsby, Cynthia, Hlavacek, Anthony M., Mohun, Timothy J.

Journal:

Cardiology in the Young

Year:

2015

Language:

english

File:

PDF, 48 KB

english, 2015

45

Use of Mechanistic Models to Integrate and Analyze Multiple Proteomic Datasets

Stites, Edward C., Aziz, Meraj, Creamer, Matthew S., Von Hoff, Daniel D., Posner, Richard G., Hlavacek, William S.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 919 KB

english, 2015

46

The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems

Yang, Jin, Hlavacek, William S

Journal:

Physical Biology

Year:

2011

Language:

english

File:

PDF, 447 KB

english, 2011

47

Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing

Nemenman, Ilya, Faeder, James R, Hlavacek, William S, Jiang, Yi, Wall, Michael E, Zilman, Anton

Journal:

Physical Biology

Year:

2011

Language:

english

File:

PDF, 716 KB

english, 2011

48

Special section dedicated to The Sixth q-bio Conference: meeting report and preface

Nemenman, Ilya, Gnanakaran, S, Munsky, Brian, Wall, Michael E, Jiang, Yi, Hlavacek, William S, Faeder, James R

Journal:

Physical Biology

Year:

2013

Language:

english

File:

PDF, 184 KB

english, 2013

49

The Fifth Annual q-bio Conference on Cellular Information Processing

Nemenman, Ilya, Gnanakaran, S, Hlavacek, William S, Jiang, Yi, Munsky, Brian, Wall, Michael E, Faeder, James R

Journal:

Physical Biology

Year:

2012

Language:

english

File:

PDF, 418 KB

english, 2012

50

An Interaction Library for the FcÎµRI Signaling Network

Chylek, Lily A., Holowka, David A., Baird, Barbara A., Hlavacek, William S.

Journal:

Frontiers in Immunology

Year:

2014

Language:

english

File:

PDF, 2.89 MB

english, 2014

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